Unless the lenses have been changed, the autofocus should stay the same. The way I used to do it was to focus with the head down sufficiently to give me a 5x7 on the easel, tighten the set screw on the lens and then shift it to 11x14 and see if the focus stayed put. Occasionally you have to reset either the 5x7 or the 1x 14 a couple of times to get it right. Once that is done, stick a negative in the holder and print first at the 5x7 setting and set the focus with a grain focusser. Do three prints, the 1st one dead on according to the grain focussing and the "tweak" the lens by very slightly turn it one way, do another print and the do a tweak the other way. Now check which print is the sharpest. Part of your shift has to do with the papers sesitivity (multigrade is more sensitive to blue light and there is a small shift in focus). Do the same test with the enlarger in the 11x14 position.You can use the same size paper, just check the centre and stick some 5x7 at the edges too. The latter will tell you if everything is aligned. This sounds a bit cumbersome, but once a IIc is set up, you really dont have worry about it again for many years.
I did get rid of my IIc several years ago as i kept buyng various 120 film cameras and playing with them (i did have the elusive Focotar-2 100/5.6 on it). By keeping the Ic only i am limited to 35mm and the temptation is removed (so far it has worked, but I still miss the IIc - it is a case of overengineered and overbuilt piece of darkroom equipment that has not been equalled. All right, the Durst 138 comes close, but wont fit in my darkroom),
I do have a IIc but it is a ultra high resolution ELCAN, based on a IIc chassi with a point source light and a 15" stack of hand ground aspherical condensors above and below the negative stage. Unforunately the 1974 vintage electronic shutter and light control has bit the dust and i have not bothered to replace it with the UniBlitz laser shutter control that would work. With the correct lens this enlarger will give you 250 lp on the easel - about 6 times what is possible with the best conventional enlarger design! It also barely covers a 35mm negative and has to be used wide-open ( with #3 filter it will give you 11x14 printing times of 0.9 to 1.1 seconds!). You actually focus on a specific layer of grain with this beast!